LOCUS KHJ47393.1 1073 aa PRT CON 17-DEC-2014 DEFINITION Trichuris suis hypothetical protein protein. ACCESSION KN538379-149 PROTEIN_ID KHJ47393.1 SOURCE Trichuris suis (pig whipworm) ORGANISM Trichuris suis Eukaryota; Metazoa; Ecdysozoa; Nematoda; Enoplea; Dorylaimia; Trichinellida; Trichuridae; Trichuris. REFERENCE 1 (bases 1 to 2343098) AUTHORS Mitreva,M. TITLE Draft genome of Trichuris suis JOURNAL Unpublished REFERENCE 2 (bases 1 to 2343098) AUTHORS Mitreva,M., Pepin,K.H., Abubucker,S., Martin,J., Minx,P., Warren,C., Palsikar,V.B., Zhang,X., Rosa,B.A. and Wilson,R.K. TITLE Direct Submission JOURNAL Submitted (27-JAN-2014) The Genome Institute, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA COMMENT Trichuris suis contaminated a dirt lot located at the USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Disease Laboratory in Beltsville, MD since the early 1960s. Adult worms were isolated for passage from pigs placed on the lot and naturally infected. The T. suis adults were manually removed from the cecum and proximal colon tissue and cultured in vitro to release fertilized eggs that were removed after 24-48 hours and embryonated to an infective stage (Hill et al., Experimental Parasitology 77, 170-178, 1993). The strain has been actively passed in pigs one to two times per year since that time and characterized for pathogenesis in pigs (Mansfield and Urban, Veterinary Immunology and Immunopathology 50, 1-17, 1996). This strain of T. suis has also been used therapeutically in human subjects with inflammatory bowel disease (Trichuris suis therapy in Crohn's disease. Summers RW, Elliott DE, Urban JF Jr, Thompson R, Weinstock JV. Gut. 2005 Jan;54(1):87-90. The Genome Institute collaborators that provided material for the genome/transcriptome sequencing are: USDA - Urban, Jr., J.F., Hill, D. E. and Michigan State University - Mansfield L.S. The repeat library was generated using Repeatmodeler (A. Smit, R. Hubley http://www.systemsbiology.org/). The Ribosomal RNA genes were identified using RNAmmer ((http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer ) and transfer RNA's were identified with tRNAscan-SE (Lowe and Eddy, 1997). Non-coding RNAs, such as microRNAs, were identified by sequence homology search of the Rfam database (http://selab.janelia.org/software.html). Repeats and predicted RNA's were then masked using RepeatMasker (A. Smit, R. Hubley & P. Green http://repeatmasker.org). Protein-coding genes were predicted using a combination of ab initio programs Snap (I. Korf, 2004), Fgenesh (Softberry, Corp) and Augustus (M. Stanke, et. Al 2008) and the annotation pipeline tool Maker (M. Yandell et. al., 2007) which aligns mRNA, EST and protein information from same species or cross-species to aid in gene structure determination and modifications. A consensus gene set from the above prediction algorithms was generated, using a logical, hierarchical approach developed at the Genome institute. Gene product naming was determined by BER (JCVI: http://ber.sourceforge.net). Our goal is to explore this WGS draft sequence of Trichuris suis to better define proteins involved in nematode parasitism that impact health and disease and are relevant to both host-parasite relationships and basic biological processes. For information regarding this assembly or project, or any other GSC genome project, please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person. For specific questions regarding the Trichuris suis genome project contact Makedonka Mitreva (mmitreva@genome.wustl.edu) at Washington University School of Medicine. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) provided funds for this project. ##Genome-Assembly-Data-START## Finishing Goal :: High-Quality Draft Current Finishing Status :: High-Quality Draft Assembly Method :: ALLPATHS_LG v. 2012-11-02 Assembly Name :: T_suis_1.0.allpaths Genome Coverage :: 392x Sequencing Technology :: Illumina ##Genome-Assembly-Data-END## FEATURES Qualifiers source /organism="Trichuris suis" /mol_type="genomic DNA" /submitter_seqid="T_suis-1.0_Cont4" /isolation_source="cecum and proximal colon of infected animals which were naturally infected" /host="Sus scrofa (pig)" /db_xref="taxon:68888" /chromosome="Unknown" /dev_stage="adult" /country="USA: Beltsville, MD" protein /locus_tag="D918_02253" intron_pos 22:1 (1/20) intron_pos 57:0 (2/20) intron_pos 105:0 (3/20) intron_pos 130:0 (4/20) intron_pos 153:0 (5/20) intron_pos 192:2 (6/20) intron_pos 238:1 (7/20) intron_pos 260:0 (8/20) intron_pos 285:1 (9/20) intron_pos 321:0 (10/20) intron_pos 343:0 (11/20) intron_pos 405:0 (12/20) intron_pos 642:0 (13/20) intron_pos 671:2 (14/20) intron_pos 733:0 (15/20) intron_pos 790:1 (16/20) intron_pos 899:2 (17/20) intron_pos 932:2 (18/20) intron_pos 990:0 (19/20) intron_pos 1036:2 (20/20) BEGIN 1 MRQEASTKTE VEGLPHCHPP SGISFGCNGR DSLMKGLCSQ KPLEWVSSLI ARFEEQLPVK 61 TGPLKNETRL LLEQSQACLV NVSKLKFSMV VGGLIRVLQM VNSMKTCSEQ DLFDSQCFIL 121 DTLEQCLAGP QDTSSHLDEE NNVKLIVQEM CKFIQIPVDS NQAIQLKGKA SKVLYGLSIS 181 SFDLIFSRIV FRLKSMSTDT SSASLSGDVG LGIGDAVDIE LMQYIHFDLK ALIKLLREIS 241 YYRPFRKDNN QVLFNSIENA IWNWMDTYPD RYYDLQITQN RELDECCYRL FDQLDSFAAE 301 SSKRRSSIWP LQMMLLILCP KTFQELRSIK PNAPCQLRLE KQKLFLQSIE KTLTMGHAHA 361 TKHHLLAAAC VAGAKLCKAA TYINVADPDN VFFSILQTMI DEVKSYLFSA TKPLFKNLPS 421 VQELDVMIEC FVALFRLNHN NEVFRVCLDT HATIPHRLVL VMALYRIAVQ TRLPWWPKID 481 LVYSRSEELV QIFNETLNNV CQGARNAFVL PSSTSIAISS HMPLRVTQSL HKMTGKLKDK 541 SITVCSGLSY PGSIAGYAIN LSSAEDATSC RQLLFWLIRL MCIEPKLFLR PAQGAASAAI 601 SVVREQSVEQ RSSCTSEVVN GLVSLIVSSS EMPELAQEAM EAVLCLHQPE NVELWQLASL 661 SATIQSLWHI SSQLLFHVCQ KLLHFQLGNF SEVLRWLRQL LVYRNLFLMN HREIANYGSG 721 DLLCKQAAEK LETVCFVYLW SLDNDAAITA LSLFRVMCEE AEIRCSSDEL PAEYVHHAEL 781 ANATNLPTVG RAVLQKSINS YLKKLTVPTT GCRQAWEDTY RYWVAFTKFL KSFPKSKFDE 841 SLQMVEMLTK QMMDRNSTRG SELNLQMVIK LWANMTGFLC ATGGVVLQTS ACVNSDLYAP 901 VTKLNPIVDN EKNVHSVEFS LPNQDILCSV ASFLNQLLSL LLIPSQKLEA SILRHVKELC 961 SYELHVSLIG HFFEQIHSVT NRFSDDTGQV NICSQNTDFV EHVVYVMKNV LLNCSKLDAR 1021 TTQLVCIEPI MLNLCKYAHV LEVGSQAFTI KSKICQLIKV VIQSFVSHFI PFE //